Trends in ultrasensitive proteomics.

Here we review recent developments and trends in sample preparation, pre-fractionation, chromatography and mass spectrometry contributing towards the ultra-sensitive global analysis of proteins. Highly sensitive MS-based proteomics is not only beneficiary for the proteome analysis of single cells, an aim which is getting into reach, but also clearly relevant for the analysis of (a) subcellular organelles, (b) specific low-abundant cell-types such as adult stem cells, and (c) smaller but more homogeneous cell populations sorted or dissected from (diseased) tissue.

[1]  Hans Clevers,et al.  Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells , 2010, Cell.

[2]  Dennis Brown,et al.  Proteomic analysis of V-ATPase-rich cells harvested from the kidney and epididymis by fluorescence-activated cell sorting. , 2010, American journal of physiology. Cell physiology.

[3]  Edward L. Huttlin,et al.  A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression , 2010, Cell.

[4]  J. Sweedler,et al.  Profiling metabolites and peptides in single cells , 2011, Nature Methods.

[5]  G. McAlister,et al.  Decision tree–driven tandem mass spectrometry for shotgun proteomics , 2008, Nature Methods.

[6]  B. Chait Mass spectrometry in the postgenomic era. , 2011, Annual review of biochemistry.

[7]  R. Templer,et al.  A first step towards practical single cell proteomics: a microfluidic antibody capture chip with TIRF detection. , 2011, Lab on a chip.

[8]  O. Ornatsky,et al.  Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry. , 2009, Analytical chemistry.

[9]  R. Chakraborty,et al.  Use of immunomagnetic separation for the detection of Desulfovibrio vulgaris from environmental samples. , 2011, Journal of microbiological methods.

[10]  S. Mohammed,et al.  Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. , 2011, Journal of proteome research.

[11]  Sean C. Bendall,et al.  Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum , 2011, Science.

[12]  Matthias Mann,et al.  Proteome Analysis of Separated Male and Female Gametocytes Reveals Novel Sex-Specific Plasmodium Biology , 2005, Cell.

[13]  B. Simons,et al.  Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). , 2011, Analytical chemistry.

[14]  Richard D. Smith,et al.  Pressurized Pepsin Digestion in Proteomics , 2010, Molecular & Cellular Proteomics.

[15]  Ruedi Aebersold,et al.  High-throughput generation of selected reaction-monitoring assays for proteins and proteomes , 2010, Nature Methods.

[16]  Sören-Oliver Deininger,et al.  MALDI imaging combined with hierarchical clustering as a new tool for the interpretation of complex human cancers. , 2008, Journal of proteome research.

[17]  J. Yates,et al.  Mass spectrometry for proteomics. , 2008, Current opinion in chemical biology.

[18]  D. Figeys,et al.  Improved Recovery and Identification of Membrane Proteins from Rat Hepatic Cells using a Centrifugal Proteomic Reactor* , 2011, Molecular & Cellular Proteomics.

[19]  L. F. Waanders,et al.  Quantitative proteomic analysis of single pancreatic islets , 2009, Proceedings of the National Academy of Sciences.

[20]  Masaru Tomita,et al.  Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines. , 2011, Analytical chemistry.

[21]  J. Foekens,et al.  NanoLC‐FT‐ICR MS improves proteome coverage attainable for ∼3000 laser‐microdissected breast carcinoma cells , 2007, Proteomics.

[22]  C. Maley,et al.  Cancer is a disease of clonal evolution within the body1–3. This has profound clinical implications for neoplastic progression, cancer prevention and cancer therapy. Although the idea of cancer as an evolutionary problem , 2006 .

[23]  John R Yates,et al.  Proteomics by mass spectrometry: approaches, advances, and applications. , 2009, Annual review of biomedical engineering.

[24]  Mingsheng Zhang,et al.  Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. , 2011, Cancer research.

[25]  A. van Oudenaarden,et al.  Noise Propagation in Gene Networks , 2005, Science.

[26]  B. Domon,et al.  Selected reaction monitoring applied to proteomics. , 2011, Journal of mass spectrometry : JMS.

[27]  André M Deelder,et al.  Imaging mass spectrometry of myxoid sarcomas identifies proteins and lipids specific to tumour type and grade, and reveals biochemical intratumour heterogeneity , 2010, The Journal of pathology.

[28]  T. Köcher,et al.  Ultra-high-pressure RPLC hyphenated to an LTQ-Orbitrap Velos reveals a linear relation between peak capacity and number of identified peptides. , 2011, Analytical chemistry.

[29]  R. Bischoff,et al.  Multidimensional chromatography coupled to mass spectrometry in analysing complex proteomics samples. , 2010, Journal of separation science.

[30]  S. Mohammed,et al.  Automated Online Sequential Isotope Labeling for Protein Quantitation Applied to Proteasome Tissue-specific Diversity*S , 2008, Molecular & Cellular Proteomics.

[31]  Matthias Mann,et al.  High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. , 2011, Journal of proteome research.

[32]  M. Mann,et al.  Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. , 2010, Immunity.

[33]  S. Mohammed,et al.  Strong cation exchange (SCX) based analytical methods for the targeted analysis of protein post-translational modifications. , 2011, Current opinion in biotechnology.

[34]  Daniel Figeys,et al.  Uncovering the Proteome Response of the Master Circadian Clock to Light Using an AutoProteome System* , 2011, Molecular & Cellular Proteomics.

[35]  M. Mann,et al.  Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer* , 2011, Molecular & Cellular Proteomics.

[36]  M. Mann,et al.  Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation* , 2011, Molecular & Cellular Proteomics.

[37]  M. Mann,et al.  System-wide Perturbation Analysis with Nearly Complete Coverage of the Yeast Proteome by Single-shot Ultra HPLC Runs on a Bench Top Orbitrap* , 2011, Molecular & Cellular Proteomics.

[38]  Peter K. Sorger,et al.  Measuring and Modeling Apoptosis in Single Cells , 2011, Cell.

[39]  Richard D. Smith,et al.  On-line digestion system for protein characterization and proteome analysis. , 2008, Analytical chemistry.

[40]  J. Foekens,et al.  NanoLC-FT-ICR MS improves proteome coverage attainable for approximately 3000 laser-microdissected breast carcinoma cells. , 2007, Proteomics.

[41]  S. Lemeer,et al.  The phosphoproteomics data explosion. , 2009, Current opinion in chemical biology.

[42]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[43]  Hans Clevers,et al.  Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling , 2011, Nature.

[44]  Didier Samuel,et al.  Identification of Cellular Targets in Human Intrahepatic Cholangiocarcinoma Using Laser Microdissection and Accurate Mass and Time Tag Proteomics* , 2010, Molecular & Cellular Proteomics.

[45]  S. Mohammed,et al.  Zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC and ZIC-cHILIC) provide high resolution separation and increase sensitivity in proteome analysis. , 2011, Analytical chemistry.

[46]  M. Mann,et al.  Quantitative, high-resolution proteomics for data-driven systems biology. , 2011, Annual review of biochemistry.

[47]  H. Clevers,et al.  Highly sensitive proteome analysis of FACS-sorted adult colon stem cells. , 2011, Journal of proteome research.

[48]  R. Aebersold,et al.  Mass spectrometry in proteomics. , 2001, Chemical reviews.

[49]  Albert J R Heck,et al.  Enhancing the Identification of Phosphopeptides from Putative Basophilic Kinase Substrates Using Ti (IV) Based IMAC Enrichment* , 2011, Molecular & Cellular Proteomics.

[50]  Wei Liu,et al.  Sample preparation method for isolation of single‐cell types from mouse liver for proteomic studies , 2011, Proteomics.

[51]  M. Moran,et al.  Large-scale mapping of human protein–protein interactions by mass spectrometry , 2007, Molecular systems biology.

[52]  L. F. Waanders,et al.  A Novel Chromatographic Method Allows On-line Reanalysis of the Proteome*S⃞ , 2008, Molecular & Cellular Proteomics.